The accord grants South American nations, renowned for their fertile land and skilled farmers, increased access at a preferential tax rate to Europe's vast market for agricultural goods.
French Agriculture Minister Annie Genevard has publicly opposed the EU-Mercosur trade agreement, citing risks of deforestation and health concerns linked to hormone-treated meat.
Official figures have recorded nearly 73,000 forest fires in Brazil over the first eight months of the year -- the highest number for any year since 2013.
A French presidential official said Brazil's comments and policies over the last weeks showed that Bolsonaro did not want to respect obligations on climate change.
French farmers for years has denounced the trade deal with the Mercosur nations of Brazil, Argentina, Bolivia, Paraguay and Uruguay, arguing that the deal would hurt French farmers’ livelihoods.